2. Software Development

2.1 Applications

Alan has also corrected edialign which crashed if the
maximum fragment size was greater than 40. This was a fixed size
memory allocation bug in the original dialign code.

Patches are available on the FTP server for all Alan's fixes.

Tim Carver has requested a change to restrict to knockout
restriction sites that are methylated by the dcm and dam methylase
systems. Other programs needing the same capability are
restover, remap and showseq. A methylase data
file will be needed with patterns for the methylase target
site. Internally, the methylated base is replaced by 'N' which is not
accepted by any restriction site. We need to check whether methylation
of one strand prevents a cut in both stands at the restriction site.

2.2 Libraries

Alan has modified parsing of Entrez output to remove an extra
line (reported by Guy Bottu).

Alan reported that the latest MACOSX compiler issues 3 warnings
for print statements with no format string in plplot and AJAX.

2.3 SoapLab

Mahmut reported on typed interfaces issues of tomcat deployment
and maven. He will ask a user to test using ant to build SoapLab.

Martin Senger will visit on June 2nd.

The production server will be updated with the namespace changed from
embossws to soaplab.ebi.ac.uk with the organizationname substituted by
an include file. This should be completed later in the week.

Tests using the RunAndWaitFor method have timed out. The server runs
and completes, but the apache gives a timeout to the client. This
method could return a report before the timeout to say the service is
still running.

2.4 Other

Alan has updated the X11 configuration to use CFLAGS, and made
modifications to find the X11 libraries on MACOSX.

the data archiving of short reads (the Short Reads Archive) and
transcriptomics expression data

maq alignment to a reference genome sequence

velvelt graph-based short read assembly

Mahmut suggested generating a Jemboss client with jar
files. This needs a known location for libajax and libnucleus unless
the JNI dependencies are removed. We need to check whether some JNI
dependencies remain.

3. Administration

Alan has a license todownload the MacOSX 10.5.6 "snow leopard" release. A new download is now available.

Alan has drafted a server specification for Peter to
review. The disks are SAS (serially attached SCSI) which are faster
than SATA. The cost is about £500/TB. We have a budget of £7.5k for
the server and £12.5k for disks although we have felixibility. We
should be able to afford about 16TB of disk. The processor
specification is 2 quad core processors, preferably (for large
indexing jobs and multiple logins) with multiple disk
channels. Alteratively we could use a separate smaller machie for the
index building tests.

Alan reported that the 3TB disk array failed to survive the
data centre power failure. Gavin will remove the failed components and
hand over to us for testing. The cause is probably a disk failure.
It seems sensible to replace all the aging disks.

Peter reported that the new grant has started on 1st May. We
have a Scientific Advisory Board. Peter will contact them with
the good news and ask about availability for an SAB meeting in
September.

4. Documentation and Training

4.1 Books

We have a meeting with the publishers on Friday. We will have a
separate meeting on Thursday to discuss the details of the remaining
tasks on the books.

Peter will revise the Developers manual, and Alan will review it.

Peter will review the User manual. Alan has some updates
from Lisa for her chapter.

4.2 Website

Peter will start to populate the wiki with information for the
SAB and plans for development under the new grant.

noted that some links are mssing on the documentation, for
example in EMBASSY packages and applications. Peter will update
the validation script and check through the site.

5. User queries and answers

Alan has fixed a remap bug reported by Jean Mao

edialign is patched to have the "aligned" attribute set for the output.

6. AOB

None.

7. Date Of Next Meeting

Future meetings will be weekly at the usual time (10am on Mondays) in
the Hall View Room. Alan will chair the meetings. Long
technical discussions can continue after the meeting.

Next week is the EMBRACE AGM and review. Peter and Mahmut are at a
meeting on Monday 18th. The next meeting will be on Tuesday 19th May.